File newFile = new File("myNewFile.mxd");
MapDocument mapDocument = new MapDocument();
mapDocument.esri_new(newFile );
/* if you will save some content in it, just comment below out
mapDocument.replaceContents(map);
mapDocument.setActiveView(map); or mapDocument.setActiveView(pageLayout);
*/
mapDocument.save(false, false);
mapDocument.close();